Tweak Vault guide's reading flow

[robszumski]

• Add $ to all commands. There are a few combo lines so being consistent makes this most clear
• Collapse a few sentences into paragraphs vs single lines
• hide key creation steps by default
• use link references when applicable
• be explicit about enclaver build -f manifest.yaml even when -f enclaver.yaml is able to be inferred
• fix some indenting for nested lists
• for complex commands, separate flags on to their own lines